Variant report

Variant	rs4656972
Chromosome Location	chr1:160921360-160921361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:160921280-160921430	NHDF-neo	bronchial:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
2	EP300	chr1:160921182-160921451	K562	blood:	n/a	n/a
3	CTCF	chr1:160921280-160921430	HepG2	liver:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
4	RAD21	chr1:160921113-160921520	HepG2	liver:	n/a	chr1:160921343-160921357
5	CTCF	chr1:160921280-160921430	BE2_C	brain:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
6	CTCF	chr1:160921300-160921450	HL-60	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
7	CTCF	chr1:160921260-160921410	AG10803	skin:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
8	CTCF	chr1:160921095-160921501	HepG2	liver:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
9	CTCF	chr1:160921226-160921487	Hela-S3	cervix:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
10	CTCF	chr1:160921171-160921501	K562	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
11	CTCF	chr1:160921300-160921450	HCT-116	colon:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
12	CTCF	chr1:160921237-160921521	Fibrobl	skin:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
13	CTCF	chr1:160921260-160921410	AG04450	lung:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
14	CTCF	chr1:160921260-160921410	HEK293	kidney:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
15	CTCF	chr1:160921280-160921430	GM12865	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
16	RAD21	chr1:160921164-160921525	IMR90	lung:	n/a	chr1:160921343-160921357
17	CTCF	chr1:160921280-160921430	Caco-2	colon:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
18	CTCF	chr1:160921260-160921410	GM12873	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
19	CTCF	chr1:160921300-160921450	HCM	heart:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
20	CTCF	chr1:160921025-160921512	A549	lung:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
21	CTCF	chr1:160921126-160921519	T-47D	breast:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
22	CTCF	chr1:160921300-160921450	GM12870	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
23	CTCF	chr1:160921280-160921430	HMF	breast:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
24	CTCF	chr1:160921300-160921450	GM12874	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
25	CTCF	chr1:160921149-160921464	A549	lung:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
26	FOS	chr1:160921309-160921551	MCF10A-Er-Src	breast:	n/a	n/a
27	JUND	chr1:160921247-160921501	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr1:160921280-160921430	GM12875	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
29	CTCF	chr1:160921300-160921450	HFF	foreskin:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
30	CTCF	chr1:160921240-160921390	HFF-Myc	foreskin:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
31	RAD21	chr1:160921175-160921578	H1-hESC	embryonic stem cell:	n/a	chr1:160921343-160921357
32	CTCF	chr1:160921280-160921430	GM12864	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
33	CTCF	chr1:160921320-160921470	WI-38	lung:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
34	CTCF	chr1:160921244-160921464	SK-N-SH_RA	brain:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
35	RAD21	chr1:160921010-160921605	H1-hESC	embryonic stem cell:	n/a	chr1:160921343-160921357
36	CTCF	chr1:160921227-160921493	Pancreas_OC	pancreas:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
37	RAD21	chr1:160921074-160921639	HCT-116	colon:	n/a	chr1:160921343-160921357
38	YY1	chr1:160921149-160921461	GM12878	blood:	n/a	n/a
39	SMC3	chr1:160921112-160921669	SK-N-SH	brain:	n/a	chr1:160921343-160921357
40	MAX	chr1:160921132-160921588	MCF-7	breast:	n/a	n/a
41	CTCF	chr1:160921260-160921410	AG04449	skin:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
42	CTCF	chr1:160921242-160921530	GM12891	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
43	CTCF	chr1:160921240-160921390	HRE	kidney:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
44	CTCF	chr1:160921240-160921390	GM12875	blood:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
45	CTCF	chr1:160921280-160921430	HEEpiC	esophagus:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
46	WRNIP1	chr1:160921203-160921672	GM12878	blood:	n/a	n/a
47	NRF1	chr1:160921202-160921521	GM12878	blood:	n/a	n/a
48	CTCF	chr1:160921226-160921492	MCF-7	breast:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
49	CTCF	chr1:160921118-160921557	MCF-7	breast:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359
50	CTCF	chr1:160921260-160921410	HEEpiC	esophagus:	n/a	chr1:160921342-160921358 chr1:160921357-160921370 chr1:160921341-160921359

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160651384..160651939-chr1:160921268..160921800,2	K562	blood:

Variant related genes	Relation type
ITLN2	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10908815	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11265522	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11265526	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11265533	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11265534	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265535	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11805631	0.80[AMR][1000 genomes]
rs12126310	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1981048	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184066	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28368883	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34655593	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3829790	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3928803	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3928804	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656968	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656971	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61802165	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656769	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680969	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691389	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7526396	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs955615	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656972	RP11-312J18.6	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160916600-160921800	Enhancers	Fetal Intestine Large	intestine
2	chr1:160916800-160923800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:160917600-160921800	Enhancers	A549	lung
4	chr1:160918000-160921400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:160918000-160923800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:160918200-160923800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:160918400-160921600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:160919000-160924000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:160919000-160924400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:160919400-160921800	Enhancers	Fetal Intestine Small	intestine
11	chr1:160919400-160923000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:160919600-160921600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:160919600-160921600	Enhancers	NHEK	skin
14	chr1:160919600-160924200	Enhancers	HMEC	breast
15	chr1:160919800-160921800	Enhancers	Ovary	ovary
16	chr1:160919800-160921800	Enhancers	Right Atrium	heart
17	chr1:160919800-160923200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:160919800-160924000	Weak transcription	Fetal Heart	heart
19	chr1:160920000-160921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:160920000-160923600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:160920200-160924200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:160920400-160921400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:160920400-160921400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:160920600-160921400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:160920600-160922800	Weak transcription	Right Ventricle	heart
26	chr1:160920800-160921400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:160920800-160921800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:160920800-160921800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:160920800-160921800	Enhancers	Esophagus	oesophagus
30	chr1:160920800-160921800	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:160921000-160921400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:160921000-160921600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:160921000-160921600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:160921000-160921600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr1:160921000-160921600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:160921000-160921600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:160921000-160921600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:160921000-160921600	Enhancers	HepG2	liver
39	chr1:160921000-160922400	Enhancers	Fetal Thymus	thymus
40	chr1:160921200-160921400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:160921200-160921600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr1:160921200-160921600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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